From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Mar 27 2008 - 06:43:41 CDT

On Thu, 27 Mar 2008, Ben Chern wrote:

BC> As I don't major in Chemistry and Biology, I don't know the answer

nobody is perfect. ;-)

BC> before. But now, I know what the difficulty is.

hmmmm....

BC> If I want to visualize the interactions responsible for the primary
BC> and secondary structure, would you give me some advice or suggestion? Is

primary structure is in the broadest sense the bonding
and thus a given input (unless you have a chemical reaction
that breaks and forms bonds).

if there was a clean answer to what determines the secondary
structure, a lot of researchers would have to look for new
projects. in principle, everything contributes and how this
can be decomposed into individual contributions, depends a
lot on the level of detail you put into the model describing
those interactions.

BC> there any reviews whick can help me understand the problem?
BC> Thank you very much.

i think you need to learn, how molecular simulations as a
whole do work. for that a text book like
 
A. R. Leach
Molecular Modeling - Principles and Applications
Prentice-Hall, 2001

may be a good starting point.

cheers,
   axel.

BC>
BC> On Thu, Mar 27, 2008 at 12:19 PM, Axel Kohlmeyer <
BC> akohlmey_at_cmm.chem.upenn.edu> wrote:
BC>
BC> > On Thu, 27 Mar 2008, Ben Chern wrote:
BC> >
BC> > BC> Hello,
BC> > BC> as we know, the interactions between different part is the reason of
BC> > the
BC> > BC> protein conformation.
BC> > BC> Then can VMD detect and show the interactions that is reponsible for
BC> > the
BC> > BC> protein conformation in every scale(primary, secondary, tertiary and
BC> > BC> quarternary structure)?
BC> >
BC> > of course not. VMD is a _visualization_ program. it only shows
BC> > information that you feed it. the interactions itself have to
BC> > be modeled with some method (forcefield, quantum chemistry etc.).
BC> >
BC> > those are a complex interplay of multiple types of interactions
BC> > (short range and long range) and "volume" and/or entropy. if you
BC> > could disentangle it that easily there would be no reason for
BC> > projects like folding_at_home and so on...
BC> >
BC> > cheers,
BC> > axel.
BC> >
BC> > --
BC> > =======================================================================
BC> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
BC> > Center for Molecular Modeling -- University of Pennsylvania
BC> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
BC> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
BC> > =======================================================================
BC> > If you make something idiot-proof, the universe creates a better idiot.
BC> >
BC>
BC>
BC>
BC>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.